South Africa A pacemen Anrich Nortje and Marco Jansen shared three wickets each, triggering a middle-order collapse to help the team win the game by four runs via DL method.
Earlier, sent in to bat by the home team captain Shreyas Iyer, South Africa 'A' made 137 for one in 25 overs in a rain-affected game.
Indian opener Shikhar Dhawan has had a frustrating tour to the West Indies and will aim to find his mojo as he joins India A squad for the remainder of the series against South Africa A.
Shivam Dube smashed a quickfire 45 off 28, while Manish Pandey scored 81 in 58 deliveries to guide India A to their third consecutive victory over South Africa A, sealing the series.
Indian youngster Shubman Gill and Wriddhiman Saha are named the captains of India A for the two four-day games against South Africa A.
Ishan Kishan scored 55 off just 24 balls as India A defeated South Africa A by two wickets in the second game of the ongoing one-day series.
Live Streaming India A vs South Africa A: Here are the details of when and where to watch IND A vs SA A 2nd One Day live match on Hotstar and Star Sports 1.
Shubman Gill has been in good form for India A while Vijay Shankar returns from injury, which forced him to return home midway from the World Cup.
Rising talent Shubman Gill is there in both Pandey's and Iyer's teams and so are Vijay Shankar, Anmolpreet Singh, Ricky Bhui, Shardul Thakur, Axar Patel and Nitish Rana.
South Africa A resumed the third and penultimate day at 219/3, 126 runs behind India A's total of 345, with Rassie van der Dussen and Rudi Second on 18 and 35 respectively.
Fast bowler Duanne Olivier was the wrecker-in-chief as he claimed six wickets to trigger the India collapse after the hosts resumed at overnight 322 for four.
The former India captain said the leg spinner has the skills and has been given the chance to prove himself in the ongoing 'A' series against South Africa.
However, it was a toil for the India A bowlers on the final day as it took them 88.5 overs to get the final six wickets.
When stumps were taken due to bad light, the visitors were trailing by 239 runs after India A declared their first innings at 584 for eight.
Leg-spinner Yuzvendra Chahal picked up one as India kept a tight leash on the South Africans, who opted to bat after winning the toss.
It is widely believed that Chahal is being kept match-ready as the selectors have named senior squad for only three Test matches in England.
Promising top-order batsman Shreyas Iyer will lead the India A team in the four-day games against the South Africans and the shift was made due to citing of heavy rains during the matches.
There is a school of thought that Ravindra Jadeja will be slowly eased out of the longer version if Chahal is able to show his skills in the four-day games.
Ravikumar Samarth was dismissed by fast bowler Dane Paterson after scoring 77 off 113 balls, Iyer remained unbeaten on 56 off 74 balls.
Mumbai batsman Shreyas Iyer delivered when it mattered most as India 'A' outplayed South Africa 'A' by seven wickets to retain the tri-series trophy they won four years ago.
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